# HG changeset patch
# User iuc
# Date 1725765719 0
# Node ID b5f87b4cfda68ac25d1c8b81d33da821a84ed159
# Parent  d90472d5f10aa7c1ecb864ccb848290f2a6eb1a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r d90472d5f10a -r b5f87b4cfda6 macros.xml
--- a/macros.xml	Mon Aug 15 09:07:14 2022 +0000
+++ b/macros.xml	Sun Sep 08 03:21:59 2024 +0000
@@ -5,8 +5,15 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.15.1</token>
-    <token name="@PROFILE@">20.05</token>
+    <!-- NOTE: for some tools only the version of the requirement but not the
+        tool's version is controlled by the TOOL_VERSION token 
+        (because their version is ahead of the requirement version .. 
+         please only bump the minor version in order to let the requirement
+         version catch up eventually). To find the tools check:
+        `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
+    <token name="@TOOL_VERSION@">1.20</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
@@ -212,37 +219,7 @@
 
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @misc{SAM_def,
-                title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/},}
-            </citation>
-            <citation type="doi">10.1093/bioinformatics/btp352</citation>
-            <citation type="doi">10.1093/bioinformatics/btr076</citation>
-            <citation type="doi">10.1093/bioinformatics/btr509</citation>
-            <citation type="bibtex">
-                @misc{Danecek_et_al,
-                Author={Danecek, P., Schiffels, S., Durbin, R.},
-                title={Multiallelic calling model in bcftools (-m)},
-                url = {http://samtools.github.io/bcftools/call-m.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Durbin_VCQC,
-                Author={Durbin, R.},
-                title={Segregation based metric for variant call QC},
-                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Li_SamMath,
-                Author={Li, H.},
-                title={Mathematical Notes on SAMtools Algorithms},
-                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{SamTools_github,
-                title={SAMTools GitHub page},
-                url = {https://github.com/samtools/samtools},}
-            </citation>
+            <citation type="doi">10.1093/gigascience/giab008</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r d90472d5f10a -r b5f87b4cfda6 samtools_ampliconclip.xml
--- a/samtools_ampliconclip.xml	Mon Aug 15 09:07:14 2022 +0000
+++ b/samtools_ampliconclip.xml	Sun Sep 08 03:21:59 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>clip primer bases from bam files</description>
     <macros>
         <import>macros.xml</import>
@@ -29,11 +29,11 @@
         <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
         <param name="input_bam" type="data" format="bam" label="BAM file" />
         <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
-        <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
-        <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
-        <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
+        <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
+        <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
+        <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
         <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
-        <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
+        <param argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
     
     </inputs>
     <outputs>
diff -r d90472d5f10a -r b5f87b4cfda6 test-data/eboVir3.clipped.bam
Binary file test-data/eboVir3.clipped.bam has changed
diff -r d90472d5f10a -r b5f87b4cfda6 test-data/eboVir3.clipped.strand.bam
Binary file test-data/eboVir3.clipped.strand.bam has changed
diff -r d90472d5f10a -r b5f87b4cfda6 test-data/eboVir3.clipped.strand_gt30.bam
Binary file test-data/eboVir3.clipped.strand_gt30.bam has changed
diff -r d90472d5f10a -r b5f87b4cfda6 test-data/eboVir3.hardclipped.bam
Binary file test-data/eboVir3.hardclipped.bam has changed